9DVD | pdb_00009dvd

Cryo EM structure of Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270

• PDB DOI: https://doi.org/10.2210/pdb9DVD/pdb
• EM Map EMD-47201: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Henipavirus hendraense, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-07 Released: 2025-10-15 
• Deposition Author(s): Binshtein, E., Crowe, J.E.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo EM structure of Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270

Binshtein, E., Crowe, J.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 90.27 kDa 
• Atom Count: 5,965 
• Modeled Residue Count: 748 
• Deposited Residue Count: 795 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	A	429	Henipavirus hendraense	Mutation(s): 0
UniProt
Find proteins for F4YH71 (Henipavirus hendraense) Explore F4YH71  Go to UniProtKB:  F4YH71
Glycosylation
Glycosylation Sites: 5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin-B2	B	138	Homo sapiens	Mutation(s): 0  Gene Names: EFNB2, EPLG5, HTKL, LERK5
UniProt & NIH Common Fund Data Resources
Find proteins for P52799 (Homo sapiens) Explore P52799  Go to UniProtKB:  P52799
PHAROS:  P52799 GTEx:  ENSG00000125266
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P52799-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fan HENV-270 heavy chain	C [auth H]	120	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fan HENV-270 light chain	D [auth L]	108	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	G [auth A], H [auth A], J [auth A], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA (Subject of Investigation/LOI)	I [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Binshtein, E., Crowe, J.E.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release